Examples with QuantitationType ubic.gemma.model.common.quantitationtype.QuantitationType used on opensource projects

Example 56 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class GeoConverterTest method testConvertDataDoubles.

@Test
public void testConvertDataDoubles() {
    List<Object> testList = new ArrayList<>();
    testList.add("1.1");
    testList.add("2929202e-4");
    testList.add("-394949.44422");
    QuantitationType qt = QuantitationType.Factory.newInstance();
    qt.setRepresentation(PrimitiveType.DOUBLE);
    byte[] actualResult = gc.convertData(testList, qt);
    double[] revertedResult = bac.byteArrayToDoubles(actualResult);
    assertEquals(revertedResult[0], 1.1, 0.00001);
    assertEquals(revertedResult[1], 2929202e-4, 0.00001);
    assertEquals(revertedResult[2], -394949.44422, 0.00001);
}

Example 57 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class GeoSuperSeriesLoadTest method testFetchAndLoadSuperSeriesB.

/*
     * See bug 2064. GSE14618 is a superseries of GSE14613 and GSE14615. This is actually even worse, because some
     * samples were run on both platforms. This is a situation we don't really want to handle completely.
     *
     */
@Test
public void testFetchAndLoadSuperSeriesB() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("gse14618superser")));
    ee = ees.findByShortName("GSE14618");
    this.tearDown();
    // noinspection unchecked
    Collection<ExpressionExperiment> results = (Collection<ExpressionExperiment>) geoService.fetchAndLoad("GSE14618", false, true, false, true, false);
    assertEquals(1, results.size());
    ee = results.iterator().next();
    ee = ees.findByShortName("GSE14618");
    ee = ees.thawLite(ee);
    Collection<QuantitationType> qts = ee.getQuantitationTypes();
    assertEquals(1, qts.size());
    Collection<ArrayDesign> arrayDesignsUsed = ees.getArrayDesignsUsed(ee);
    Collection<ArrayDesign> others = new HashSet<>();
    others.add((ArrayDesign) arrayDesignsUsed.toArray()[1]);
    ArrayDesign arrayDesign = (ArrayDesign) arrayDesignsUsed.toArray()[0];
    ArrayDesign merged = adms.merge(arrayDesign, others, RandomStringUtils.randomAlphabetic(5), RandomStringUtils.randomAlphabetic(5), false);
    ee = eepss.switchExperimentToArrayDesign(ee, merged);
    vms.mergeVectors(ee);
    ee = ees.load(ee.getId());
    ee = ees.findByShortName("GSE14618");
    ee = ees.thaw(ee);
    assertEquals(40, ee.getProcessedExpressionDataVectors().size());
    // System.err.println( ee.getProcessedExpressionDataVectors().size() );
    boolean found1 = false;
    boolean found2 = false;
    ByteArrayConverter bac = new ByteArrayConverter();
    for (ProcessedExpressionDataVector v : ee.getProcessedExpressionDataVectors()) {
        double[] dat = bac.byteArrayToDoubles(v.getData());
        int count = 0;
        assertEquals(92, dat.length);
        if (v.getDesignElement().getName().equals("117_at")) {
            found1 = true;
            for (double d : dat) {
                if (Double.isNaN(d)) {
                    count++;
                }
            }
            assertEquals("Should have been no missing values", 0, count);
        } else if (v.getDesignElement().getName().equals("1552279_a_at")) {
            found2 = true;
            for (double d : dat) {
                if (Double.isNaN(d)) {
                    count++;
                }
            }
            assertEquals("Wrong number of missing values", 42, count);
        }
    }
    assertTrue("Didn't find first test probe expected.", found1);
    assertTrue("Didn't find second test probe expected.", found2);
}

Example 58 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class TwoChannelMissingValuesTest method testMissingValueGSE11017.

/**
 * Was giving all missing values.
 */
@Test
public void testMissingValueGSE11017() throws Exception {
    ExpressionExperiment old = eeService.findByShortName("GSE11017");
    if (old != null)
        eeService.remove(old);
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE11017.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE11017");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    ExpressionExperiment expExp = (ExpressionExperiment) ((Collection<?>) result).iterator().next();
    expExp = persisterHelper.persist(expExp, persisterHelper.prepare(expExp));
    Collection<RawExpressionDataVector> calls = tcmv.computeMissingValues(expExp, 2.0, new ArrayList<Double>());
    // print( calls );
    assertEquals(20, calls.size());
    boolean hasNewQT = false;
    Collection<QuantitationType> qts = eeService.getQuantitationTypes(expExp);
    for (QuantitationType qt : qts) {
        if (qt.getType().equals(StandardQuantitationType.PRESENTABSENT)) {
            hasNewQT = true;
            break;
        }
    }
    assertTrue(hasNewQT);
    ExpressionDataMatrixBuilder builder = new ExpressionDataMatrixBuilder(calls);
    ExpressionDataBooleanMatrix missingValues = builder.getMissingValueData();
    assertTrue(missingValues.getQuantitationTypes().iterator().next().getDescription().contains("signal threshold"));
    Boolean[][] mm = missingValues.getRawMatrix();
    boolean hasPresent = false;
    for (Boolean[] aMm : mm) {
        for (Boolean anAMm : aMm) {
            if (anAMm) {
                hasPresent = true;
                break;
            }
        }
    }
    assertTrue(hasPresent);
}

Example 59 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class MatrixConversionTest method getDesignElementDataVectors.

/**
 * Creates an ugly (but not unusual) situation where there are two bioassay dimensions with different sizes,
 * referring to the same set of biomaterials.
 *
 * @return design element data vectors
 */
private Collection<DesignElementDataVector> getDesignElementDataVectors(Collection<QuantitationType> quantTypes) {
    Collection<DesignElementDataVector> vectors = new HashSet<>();
    ArrayDesign ad = ArrayDesign.Factory.newInstance();
    ad.setName("junk");
    List<CompositeSequence> sequences = this.getCompositeSequences(ad);
    ArrayDesign adb = ArrayDesign.Factory.newInstance();
    adb.setName("bjunk");
    List<CompositeSequence> sequencesb = this.getCompositeSequences(ad);
    // resused
    List<BioMaterial> bioMaterials = this.getBioMaterials();
    for (QuantitationType quantType : quantTypes) {
        /*
             * Create two bioassay dimension which overlap; "A" does not use all the biomaterials.
             */
        BioAssayDimension baDimA = BioAssayDimension.Factory.newInstance();
        Iterator<BioMaterial> bmita = bioMaterials.iterator();
        for (long i = 0; i < MatrixConversionTest.NUM_BIOMATERIALS - 20; i++) {
            BioAssay ba = ubic.gemma.model.expression.bioAssay.BioAssay.Factory.newInstance();
            ba.setName(RandomStringUtils.randomNumeric(5) + "_testbioassay");
            ba.setSampleUsed(bmita.next());
            ba.setArrayDesignUsed(ad);
            ba.setId(i);
            baDimA.getBioAssays().add(ba);
        }
        baDimA.setName(RandomStringUtils.randomAlphanumeric(10));
        BioAssayDimension baDimB = BioAssayDimension.Factory.newInstance();
        Iterator<BioMaterial> bmitb = bioMaterials.iterator();
        for (long i = 0; i < MatrixConversionTest.NUM_BIOMATERIALS; i++) {
            BioAssay ba = ubic.gemma.model.expression.bioAssay.BioAssay.Factory.newInstance();
            ba.setName(RandomStringUtils.randomNumeric(15) + "_testbioassay");
            ba.setSampleUsed(bmitb.next());
            ba.setArrayDesignUsed(adb);
            ba.setId(i + 20);
            baDimB.getBioAssays().add(ba);
        }
        baDimB.setName(RandomStringUtils.randomAlphanumeric(10));
        // bio.a gets cs 0-99, bio.b gets 100-199.
        long j = 0;
        j = this.loopVectors(vectors, sequencesb, quantType, baDimA, j, MatrixConversionTest.NUM_CS - 100);
        // noinspection UnusedAssignment // Better readability
        j = this.loopVectors(vectors, sequences, quantType, baDimB, j, MatrixConversionTest.NUM_CS);
    }
    return vectors;
}

Example 60 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class QuantitationTypeData method getPreferredQTypes.

public List<QuantitationType> getPreferredQTypes() {
    List<QuantitationType> result = new ArrayList<>();
    List<BioAssayDimension> dimensions = this.getBioAssayDimensions();
    if (dimensions.size() == 0) {
        throw new IllegalArgumentException("No bioAssayDimensions!");
    }
    for (BioAssayDimension dimension : dimensions) {
        for (DesignElementDataVector vector : vectors) {
            if (!vector.getBioAssayDimension().equals(dimension))
                continue;
            QuantitationType qType = vector.getQuantitationType();
            if (!qType.getIsPreferred() && !qType.getIsMaskedPreferred())
                continue;
            // if we get here, we're in the right place.
            result.add(qType);
            // on to the next dimension.
            break;
        }
    }
    return result;
}